LAMMPS (15 Sep 2022)
  using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable     r0 equal  0.97
variable     d1 equal  ${r0}
variable     d1 equal  0.97
variable     d2 equal  sqrt(3.0)*${r0}
variable     d2 equal  sqrt(3.0)*0.97
variable     d3 equal  3.0*${r0}
variable     d3 equal  3.0*0.97
variable     ro equal  2./${d1}/${d2}/${d3}
variable     ro equal  2./0.97/${d2}/${d3}
variable     ro equal  2./0.97/1.68008928334181/${d3}
variable     ro equal  2./0.97/1.68008928334181/2.91

variable     T  equal  0.23
variable     LD equal  1.0

units        lj
atom_style   ellipsoid

boundary     p p p

lattice      custom ${ro} a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 2.91  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
Lattice spacing in x,y,z = 0.97 1.6800893 2.91


region       box block   0 40  0 24  -20  20
create_box   1 box
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
  1 by 1 by 1 MPI processor grid
region       membrane block  0 40  0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
  using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
  create_atoms CPU = 0.001 seconds

group        membrane  region membrane
1920 atoms in group membrane

set type 1 mass  1.0
Setting atom values ...
  1920 settings made for mass

set type 1 shape  1 1 1
Setting atom values ...
  1920 settings made for shape

set          group all quat 0 -1 0  90
Setting atom values ...
  1920 settings made for quat

#compute      memb  all temp/com
#compute      rot all temp/asphere bias memb
velocity     all create ${T} 87287 loop geom
velocity     all create 0.23 87287 loop geom

pair_style   ylz  2.6
pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
neighbor     1.0 bin


thermo_style custom step temp press pxx pyy
thermo       200

timestep     0.01

#dump         1 all atom 10 dump_onlymembrane.lammpstrj

fix          1 all langevin ${T} ${T}  ${LD}  48279
fix          1 all langevin 0.23 ${T}  ${LD}  48279
fix          1 all langevin 0.23 0.23  ${LD}  48279
fix          1 all langevin 0.23 0.23  1  48279


fix          2 all nve/asphere
run          3000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair ylz command:

@Article{Yuan10,
 author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
 title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
 journal = {Phys. Rev. E},
 year =    2010,
 volume =  82,
 pages =   {011905}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 10 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.6
  ghost atom cutoff = 3.6
  binsize = 1.8, bins = 22 23 65
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair ylz, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
   Step          Temp          Press           Pxx            Pyy      
         0   0.23          -0.0073508785  -0.012283389   -0.012234574  
       200   0.20903886    -0.0010605951  -0.0011885957  -0.00198842   
       400   0.21898026    -0.00069250685 -0.0013217981  -0.00073225707
       600   0.22689361    -0.00057919328 -0.00076880503 -0.0010242283 
       800   0.22983221    -0.00032145682 -0.00051928834 -0.00059337525
      1000   0.23819392    -0.00027969126 -0.00088082301 -5.2666567e-05
      1200   0.22053795    -0.00029571329 -0.0004446455  -0.00035529929
      1400   0.22285021    -0.0002690371  -0.00068896571 -3.6258442e-05
      1600   0.22687044     2.8599875e-05 -0.00032651798  0.0004056081 
      1800   0.23356905    -2.28742e-05   -0.00027073251  0.00025081131
      2000   0.22499821     8.8230586e-06 -7.5750159e-05  0.0001988705 
      2200   0.23162995    -9.026855e-05  -0.00025832535  5.4904927e-05
      2400   0.22920223     0.00016700455  3.5283125e-05  0.00034955857
      2600   0.2260299      5.3095557e-05  0.00025691786  0.00013353467
      2800   0.2296401      0.00043234854  0.00058344966  0.00063645193
      3000   0.22564577     2.6423111e-05  8.9918406e-05  0.00022146229
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms

Performance: 383058.431 tau/day, 443.355 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.7968     | 5.7968     | 5.7968     |   0.0 | 85.67
Neigh   | 0.086077   | 0.086077   | 0.086077   |   0.0 |  1.27
Comm    | 0.034761   | 0.034761   | 0.034761   |   0.0 |  0.51
Output  | 0.00038014 | 0.00038014 | 0.00038014 |   0.0 |  0.01
Modify  | 0.8268     | 0.8268     | 0.8268     |   0.0 | 12.22
Other   |            | 0.02181    |            |       |  0.32

Nlocal:           1920 ave        1920 max        1920 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            772 ave         772 max         772 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          46804 ave       46804 max       46804 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46804
Ave neighs/atom = 24.377083
Neighbor list builds = 99
Dangerous builds = 0


Total wall time: 0:00:06
